Biology subjects

Zielezinski, A.

Publications and source records attributed to Zielezinski, A..

12 recordsLinked to original sources

bioRxiv2026

Cosmopolitan gut bacteriophages expand the phenotype of health-related bacteria

Metagenomics has vastly expanded our knowledge of the human gut virome, yet the focus on dominant taxa has missed low-abundant but highly prevalent bacteriophages. Here, high-sensitivity taxonomic profiling of 53,976 samples from 42 countries, including non-industrialised populations and ancient DNA from five archaeological sites, reveals that only 0.3% of 64,238 phage genera are cosmopolitan, occurring in >20% of all subjects and on six continents. The most prevalent of these is Mushuvirus, with two distinct species detected in 60% of individuals, previously missed due to artefacts in reference genomes and their consistently low relative abundance (<0.8%). Population genomics shows that while one species is globally ubiquitous, the other predominates in individuals with West Eurasian ancestry. Together with 12 additional novel genera, we propose to classify these viruses into a new family Mushuviridae, found in [~]89% of studied humans. These transposable phages integrate into diverse hosts from two taxonomic orders of short-chain fatty acid-producing bacteria. Multi-omics experiments with Faecalibacterium demonstrate that hosts produce and secrete Mushuvirus-encoded receptor-binding proteins, which are actively diversified in lysogenic hosts. Together, these findings illuminate a globally distributed, active phage lineage that has persisted for millennia and continues to reshape the functional repertoire of bacteria central to human gut health.

microbiology↗

bioRxiv2025

FAMSA2 enables accurate multiple sequence alignment at protein-universe scale

We introduce FAMSA2, an algorithm that produces high-accuracy multiple protein sequence alignments with unprecedented speed. Across structural, phylogenetic, and functional benchmarks, FAMSA2 matches or exceeds the accuracy of state-of-the-art tools while running up to 400 times faster and outperforming the fastest existing aligners. The ability of FAMSA2 to process 12 million sequences in 40 minutes on a 64 GB RAM workstation enables evolutionary and structural analyses at previously unattainable scales.

bioinformatics↗

bioRxiv2024

Bacterial Lytic Polysaccharide Monooxygenases negatively affect insect larvae growth

BACKGROUNDLytic Polysaccharide Monooxygenases (LPMOs) are recently discovered redox enzymes broadly distributed across various taxa, including bacteria, fungi, and viruses. LPMO proteins can oxidatively cleave the glycosidic chains found in carbohydrate polymers, allowing efficient decomposition of recalcitrant polysaccharides such as chitin or cellulose. While LPMOs have primarily been studied for their role in biomass conversion, other biological roles of these enzymes are not well understood. RESULTSHere, we assess the influence of four different LMPOs, derived from Bacillus thuringiensis and Serratia marcescens bacteria, on Spodoptera exigua larvae. The tested proteins administered per os resulted in significant growth impairment, with the mean body weight of the treated larvae being lower than the control group by 30-69 percentage points, depending on the specific LPMO. CONCLUSIONThis work indicates that LPMO enzymes are capable of insect larvae development inhibition and thus may play an important role in insect pathogenesis caused by bacteria. Moreover, the results obtained in this study are an early sign of the potential use of LPMOs in future pest management strategies.

microbiology↗

bioRxiv2024

Ultrafast and accurate sequence alignment and clustering of viral genomes

Viromics produces millions of viral genomes and fragments annually, overwhelming traditional sequence comparison methods. We introduce Vclust, a novel approach that determines average nucleotide identity by Lempel-Ziv parsing and clusters viral genomes with thresholds endorsed by authoritative viral genomics and taxonomy consortia. Vclust demonstrates superior accuracy and efficiency compared to existing tools, clustering millions of virus genomes in a few hours on a mid-range workstation.

bioinformatics↗

bioRxiv2024

Ribosomal composition affects the noncanonical translation and toxicity of polyglycine-containing proteins in fragile X-associated conditions

Expansion of CGG repeats (CGGexp) in the 5 untranslated region (5UTR) of the FMR1 gene underlies the fragile X premutation-associated conditions including tremor/ataxia syndrome, a late-onset neurodegenerative disease and fragile X-associated primary ovarian insufficiency. One common pathomechanism of these conditions is the repeat-associated non-AUG-initiated (RAN) translation of CGG repeats of mutant FMR1 mRNA, resulting in production of FMRpolyG, a toxic protein containing long polyglycine tract. To identify novel modifiers of RAN translation we used an RNA-tagging system and mass spectrometry-based screening. It revealed proteins enriched on CGGexp-containing FMR1 RNA in cellulo, including a ribosomal protein RPS26, a component of the 40S subunit. We demonstrated that depletion of RPS26 and its chaperone TSR2, modulates FMRpolyG production and its toxicity. We also found that the RPS26 insufficiency impacted translation of limited number of proteins, and 5UTRs of mRNAs encoding these proteins were short and guanosine and cytosine-rich. Moreover, the silencing of another component of the 40S subunit, the ribosomal protein RPS25, also induced repression of FMRpolyG biosynthesis. Results of this study suggest that the two 40S ribosomal proteins and chaperone TSR2 play an important role in noncanonical CGGexp-related RAN translation.

molecular biology↗

bioRxiv2023

Ultra-conserved bacteriophage genome sequence identified in 1300-year-old human paleofaeces

Bacteriophages are widely recognised as rapidly evolving biological entities. However, we discovered an ancient genome nearly identical to present-day Mushuvirus mushu, a phage that infects commensal microorganisms in the human gut ecosystem. The DNA damage patterns of this genome have confirmed its ancient origin, and, despite 1300 years of evolution, the ancient Mushuvirus genome shares 97.7% nucleotide identity with its modern counterpart, indicating a long-term relationship between the prophage and its host. We also reconstructed and authenticated 297 other phage genomes from the last 5300 years, including those belonging to unknown families. Our findings demonstrate the feasibility of reconstructing ancient phage genomes, expanding the known virosphere, and offering new insights into phage-bacteria interactions that cover several millennia.

microbiology↗

bioRxiv2023

TRGdb: a universal resource for exploration of taxonomically restricted genes in bacteria

The TRGdb database is a resource dedicated to taxonomically restricted genes (TRGs) in bacteria. It provides a comprehensive collection of genes that are specific to different genera and species, according to the latest release of bacterial taxonomy. The user interface allows for easy browsing and searching as well as sequence similarity exploration. The website also provides information on each TRG protein sequence, including its level of disorder, complexity, and tendency to aggregate. TRGdb is a valuable resource for gaining a deeper understanding of the TRGs-associated, unique features and characteristics of bacterial organisms. The TRGdb resource is freely accessible through www.combio.pl/trgdb.

bioinformatics↗

bioRxiv2022

A ligand-receptor interactome atlas of the zebrafish

Studies in zebrafish can unravel the functions of cellular communication and thus identify novel bench-to-bedside drugs targeting cellular communication signaling molecules. Due to the incomplete annotation of zebrafish proteome, the knowledge of zebrafish receptome, secretome and tools to explore their interactome is limited. To address this gap, we de novo predicted the cellular localization of zebrafish reference proteome using deep learning algorithm. We combined the predicted and existing annotations on cellular localization of zebrafish proteins, and created repositories of zebrafish secretome, receptome, and interactome as well as associated diseases and targeting drugs. Unlike other tools, our interactome atlas is primarily based on physical interaction data of zebrafish proteome. The resources are available as R and Python scripts (https://github.com/DanioTalk). DanioTalk provides a novel resource for researchers interested in targeting cellular communication in zebrafish, as we demonstrate in applications studying synapse and axo-glial interactome.

developmental biology↗

bioRxiv2021

PHIST: fast and accurate prediction of prokaryotichosts from metagenomic viral sequences

SummaryPHIST (Phage-Host Interaction Search Tool) predicts prokaryotic hosts of viruses from their genomic sequences. It improves host prediction accuracy at species level over current alignment-based tools (on average by 3 percentage points) as well as alignment-free and CRISPR-based tools (by 14-20 percentage points). PHIST is also two orders of magnitude faster than alignment-based tools making it suitable for metagenomics studies. Availability and implementationGNU-licensed C++ code wrapped in Python API available at: https://github.com/refresh-bio/phist Contactandrzej.zielezinski@amu.edu.pl, adam.gudys@polsl.pl Supplementary informationSupplementary data are available at publisher Web site.

bioinformatics↗

bioRxiv2021

Taxonomy-aware, sequence similarity ranking reliably predicts phage-host relationships

BackgroundSimilar regions in virus and host genomes provide strong evidence for phage-host interaction, and BLAST is one of the leading tools to predict prokaryotic hosts from phage sequences. However, BLAST-based host prediction has three major limitations: (i) top-scoring sequences do not always point to the actual host, (ii) mosaic phage genomes may match to many, typically related, bacteria, and (iii) phage and host sequences may diverge beyond the point where their relationship can be detected by a BLAST alignment. ResultsWe created an extension to BLAST, named Phirbo, that improves host prediction quality beyond what is obtainable from standard BLAST searches. The tool harnesses information concerning sequence similarity and bacteria relatedness to predict phage-host interactions. Phirbo was evaluated on three benchmark sets of known phage-host pairs, and it improved precision and recall by 11-40 percentage points over currently available, state-of-the-art, alignment-based, alignment-free, and machine learning host prediction tools. Moreover, the discriminatory power of Phirbo for the recognition of phage-host relationships surpassed the results of other tools by at least 10 percentage points (Area Under the Curve = 0.95), yielding a mean host prediction accuracy of 57% and 68% at the genus and family levels respectively, and drops by 12 percentage points when using only a fraction of phage genome sequences (3 kb). Finally, we provide insights into a repertoire of protein and ncRNA genes that are shared between phages and hosts and may be prone to horizontal transfer during infection. ConclusionsOur results suggest that Phirbo is a simple and effective tool for predicting phage host relationships.

bioinformatics↗

bioRxiv2020

RaFAH: A superior method for virus-host prediction

Viruses of prokaryotes are extremely abundant and diverse. Culture-independent approaches have recently shed light on the biodiversity these biological entities1,2. One fundamental question when trying to understand their ecological roles is: which host do they infect? To tackle this issue we developed a machine-learning approach named Random Forest Assignment of Hosts (RaFAH), based on the analysis of nearly 200,000 viral genomes. RaFAH outperformed other methods for virus-host prediction (F1-score = 0.97 at the level of phylum). RaFAH was applied to diverse datasets encompassing genomes of uncultured viruses derived from eight different biomes of medical, biotechnological, and environmental relevance, and was capable of accurately describing these viromes. This led to the discovery of 537 genomic sequences of archaeal viruses. These viruses represent previously unknown lineages and their genomes encode novel auxiliary metabolic genes, which shed light on how these viruses interfere with the host molecular machinery. RaFAH is available at https://sourceforge.net/projects/rafah/.

bioinformatics↗

bioRxiv2019

Benchmarking of alignment-free sequence comparison methods

Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment. Here, we present a community resource (http://afproject.org) to establish standards for comparing alignment-free approaches across different areas of sequence-based research. We characterize 74 AF methods available in 24 software tools for five research applications, namely, protein sequence classification, gene tree inference, regulatory element detection, genome-based phylogenetic inference and reconstruction of species trees under horizontal gene transfer and recombination events. The interactive web service allows researchers to explore the performance of alignment-free tools relevant to their data types and analytical goals. It also allows method developers to assess their own algorithms and compare them with current state-of-the-art tools, accelerating the development of new, more accurate AF solutions.

bioinformatics↗